The German chancellor and president said in a statement that it was unacceptable for such hatred to develop in the country that perpetrated the Holocaust.
President Walter Steinmeier told those gathered in front of the Brandenburg Gate in Berlin: "It is intolerable that Jews are living in fear in our country again. Every attack on Jews and Jewish institutions is a disgrace for Germany. I am ashamed of every attack.
"I am outraged that anti-Semitism and inhuman agitation have erupted all over the world since 7 October, on social media and shamefully in Germany," said Chancellor Olaf Scholz.
More than 20,000 people took part in the protests, organisers said. Protesters carried posters with pictures of Israelis reported missing or held hostage by Hamas.
On Wednesday, attackers threw two Molotov cocktails at a synagogue in Berlin. Scholz strongly condemned the incident and extended security measures.
German leaders protest against rising antisemitism
On Sunday, various organisations protested in Berlin against the increase in anti-Semitic incidents following the war in Gaza.
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